updating --update and bumping nexclade and pangolin

replikation · Apr 12, 2022 · e407cbf · e407cbf
1 parent 4489f83
commit e407cbf
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -41,8 +41,8 @@ params {
     update = false
     screen_reads = false
     screen_reads_plot_cutoff = 0.03
-    defaultpangolin = 'nanozoo/pangolin-v4:4.0--1.2.133'
-    defaultnextclade = 'nanozoo/nextclade:1.10.3--2022-02-07'
+    defaultpangolin = 'nanozoo/pangolin-v4:4.0.4--1.2.133'
+    defaultnextclade = 'nanozoo/nextclade:1.11.0--2022-03-31'
 
     // parameters
     primerV = 'V3'

diff --git a/poreCov.nf b/poreCov.nf
@@ -235,7 +235,7 @@ if (params.samples) {
 
 static boolean DockernetIsAvailable() {
     try {
-        final URL url = new URL("https://registry.hub.docker.com/v2/repositories/nanozoo/pangolin/tags/");
+        final URL url = new URL("https://registry.hub.docker.com/v2/repositories/nanozoo/pangolin-v4/tags/");
         final URLConnection conn = url.openConnection();
         conn.connect();
         conn.getInputStream().close();
@@ -252,7 +252,7 @@ def internetcheck = DockernetIsAvailable()
 if (params.update) {
 println "\033[0;33mWarning: Running --update might not be poreCov compatible!\033[0m"
     if ( internetcheck.toString() == "true" ) { 
-        tagname = 'https://registry.hub.docker.com/v2/repositories/nanozoo/pangolin/tags/'.toURL().text.split(',"name":"')[1].split('","')[0]
+        tagname = 'https://registry.hub.docker.com/v2/repositories/nanozoo/pangolin-v4/tags/'.toURL().text.split(',"name":"')[1].split('","')[0]
         params.pangolindocker = "nanozoo/pangolin:" + tagname
         println "\033[0;32mFound latest pangolin container, using: " + params.pangolindocker + " \033[0m"